Pipeline scheduling with input port constraints for an FPGA-based biochemical simulator

Tomoya Ishimori, Hideki Yamada, Yuichiro Shibata, Yasunori Osana, Masato Yoshimi, Yuri Nishikawa, Hideharu Amano, Akira Funahashi, Noriko Hiroi, Kiyoshi Oguri

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

This paper discusses design methodology of high-throughput arithmetic pipeline modules for an FPGA-based biochemical simulator. Since limitation of data-input bandwidth caused by port constraints often has a negative impact on pipeline scheduling results, we propose a priority assignment method of input data which enables efficient arithmetic pipeline scheduling under given input port constraints. Evaluation results with frequently used rate-law functions in biochemical models revealed that the proposed method achieved shorter latency compared to ASAP and ALAP scheduling with random input orders, reducing hardware costs by 17.57 % and by 27.43 % on average, respectively.

Original languageEnglish
Pages (from-to)368-373
Number of pages6
JournalLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume5453
DOIs
Publication statusPublished - 2009

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Field Programmable Gate Array
Field programmable gate arrays (FPGA)
Simulator
Pipelines
Simulators
Scheduling
High Throughput
Design Methodology
Latency
Assignment
Bandwidth
Throughput
Hardware
Module
Evaluation
Costs
Model

ASJC Scopus subject areas

  • Computer Science(all)
  • Theoretical Computer Science

Cite this

Pipeline scheduling with input port constraints for an FPGA-based biochemical simulator. / Ishimori, Tomoya; Yamada, Hideki; Shibata, Yuichiro; Osana, Yasunori; Yoshimi, Masato; Nishikawa, Yuri; Amano, Hideharu; Funahashi, Akira; Hiroi, Noriko; Oguri, Kiyoshi.

In: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol. 5453, 2009, p. 368-373.

Research output: Contribution to journalArticle

Ishimori, Tomoya ; Yamada, Hideki ; Shibata, Yuichiro ; Osana, Yasunori ; Yoshimi, Masato ; Nishikawa, Yuri ; Amano, Hideharu ; Funahashi, Akira ; Hiroi, Noriko ; Oguri, Kiyoshi. / Pipeline scheduling with input port constraints for an FPGA-based biochemical simulator. In: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2009 ; Vol. 5453. pp. 368-373.
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